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Genome-wide Association Studies-GWAS01:11

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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Related Experiment Video

Updated: Jul 12, 2025

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
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The Global ALPL gene variant classification project: Dedicated to deciphering variants.

Mariam R Farman1, Catherine Rehder2, Theodora Malli3

  • 1Department of Paediatrics and Adolescent Medicine, Johannes Kepler University Linz, Linz, Austria.

Bone
|October 28, 2023
PubMed
Summary

This study reclassifies variants of uncertain significance in the ALPL gene, improving genetic diagnosis for hypophosphatasia (HPP). The ALPL gene variant database aids in understanding HPP genetic and phenotypic spectrums for better patient care.

Keywords:
ACMGAlkaline phosphataseHypophosphatasiaReclassificationVitamin B6

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Area of Science:

  • Genetics
  • Rare Diseases
  • Biochemistry

Background:

  • Hypophosphatasia (HPP) is a rare inherited disorder affecting bone and tooth mineralization, caused by pathogenic variants in the ALPL gene.
  • Variants of uncertain significance (VUS) in ALPL lead to diagnostic delays and uncertainty for patients and healthcare providers.
  • Tissue non-specific alkaline phosphatase (TNSALP) is encoded by the ALPL gene.

Purpose of the Study:

  • To reclassify Variants of Uncertain Significance (VUS) in the ALPL gene.
  • To enhance the ALPL gene variant database with updated genetic, phenotypic, and functional information.
  • To improve genetic counseling and medical decision-making for hypophosphatasia patients.

Main Methods:

  • Established an international, multidisciplinary expert consortium for variant classification.
  • Utilized a multi-step process adhering to ACMG/AMP guidelines, including clinical phenotype assessment and literature research with AI.
  • Incorporated molecular genetic assessment and in-vitro functional testing to measure ALP residual activity.

Main Results:

  • The ALPL gene variant database archives coding and non-coding variants, including SNVs, indels, and structural variants.
  • A submission system allows experts to submit VUS for classification.
  • Reclassification of VUS is performed using a rigorous, multi-faceted approach.

Conclusions:

  • The ALPL gene variant classification project and database will benefit the global medical community.
  • Characterization of new ALPL variants will broaden the understanding of the HPP genotypic and phenotypic spectrum.
  • This project may establish a gold standard for multidisciplinary variant interpretation in rare diseases.